Combine Fragments - Advanced Options Dialog Box

Combine Fragments - Advanced Options Dialog Box Features

• Linking section
• Filtering options section

Linking section

The options in this section apply when linking the fragments to a core.

Number of trials text box

Specify the number of trials to be used. In each trial, sets of fragments are chosen at random from the possible fragments, and an attempt is made to link them to each core. Each set corresponds to a particular number of fragments, from the minimum specified to the maximum. The default is 20. This default is appropriate for a small number of fragments, where it may be possible to exhaustively sample the fragments.

Minimum fragments to combine text box

Specify the minimum number of fragments to link to the core molecule. The default is 2.

Maximum fragments to combine text box

Specify the maximum number of fragments to link to the core molecule. The default is 4.

Filtering options section

In this section you can specify the values of various thresholds that are used to filter out structures with poor joining geometry, too many atoms, or are occupying the same site.

Minimum fragment centroid distance text box

Minimum distance between centroids of fragments that can be joined. Fragments whose centroids are closer than this distance are considered to occupy the same site and are therefore not candidates for joining.

Maximum bond angle deviation text box

Maximum deviation between bond directions for bonds that can be joined. If metnylene linkers are included, the test is applied between the fragments and the linkers, to ensure good geometry.

Maximum atom-atom distance text box

Maximum allowed distance between the bonding atom in one fragment and the leaving atom in the other fragment. The criterion is applied both ways.The bond lengths in each fragment are temporarily adjusted to match the ideal bond length for the new bond before the comparison is made. This adjustment ensures that the new bond length is no more than the specified distance from the ideal bond length.

Maximum number of fragment atoms text box

Specify the maximum number of atoms in any fragment. The default is 200. This threshold allows you to exclude the receptor in a pose viewer file from consideration as a fragment, for example.